ATLANTIS’ PLANET. John and Teyla are in a Puddlejumper, flying over the ocean.
SHEPPARD: Haven’t been to the mainland in a while. How’s everybody settling in?
TEYLA: Halling believes the first crops will have a good yield.
SHEPPARD: You still miss home?
TEYLA: There is still talk of returning, even though I’ve told them the Wraith have scorched Athos bare in revenge for our resistance.
SHEPPARD: Well, maybe in time this place will start to begin to feel like home.
(Teyla sees something in front of and to the right of the Jumper. She stares at it.)
TEYLA: Do you see that?
(John looks up from his controls and sees a huge black storm cloud in the distance.)
SHEPPARD: That can’t be a storm – it stretches across the whole horizon.
TEYLA: I’ve never seen something like that from so high.
SHEPPARD: I’ve seen a lot of things from this altitude, but nothing like that. (He activates comms.) Atlantis base, this is Jumper One. We’re gonna change our heading to investigate a storm.

ATLANTIS CONTROL ROOM.
WEIR (into comms): Major, this is Weir. We didn’t copy that. You’re breaking up.
SHEPPARD (over comms): I said there’s ... (static) ... ermanence headed right ... (static) ... the weather forecasting.
WEIR (to the tech sitting at the control panel): Did he just say ‘weather forecasting’?!

JUMPER ONE. The Jumper has now risen higher and is flying over the top of the cloud. From the shape of the cloud, it’s clearly a hurricane.
TEYLA: Do all storms look like this from above?
SHEPPARD: No. (He calls up a display.) This must cover twenty percent of the planet.
TEYLA: Is it headed towards the mainland?
SHEPPARD: Tracking right towards the settlement.
TEYLA (looking concerned for her people): And after that?
SHEPPARD: Straight to Atlantis.

ATLANTIS. CONFERENCE ROOM. The usual crew are present, together with Doctor Zelenka.
McKAY: This planet is basically the same size as Earth. Now, hurricanes on Earth never get as big as this bad boy because once they hit the shore, the brakes get put on. Without as much landmass to slow it down here, it’s just, uh, gaining momentum.
ZELENKA: Both of them are.
McKAY: Yes.
WEIR: Both of them?
TEYLA: We saw only one.
McKAY: It only looked like one. Now, according to the Ancient database, every twenty or thirty years the sea gets unseasonably warm. Now that, for reasons too boring to get into, means that hurricanes are much more likely to occur.
ZELENKA: Well, like El Nino, the ocean ...
McKAY (interrupting): Like I said, too boring to go into.
WEIR (sternly to the pair of them): Focus.
McKAY: Well basically, if you have a situation where there are a bunch of hurricanes out there, the likelihood of two colliding is greatly increased – that’s what’s happening.
ZELENKA: It’s more like a merger than a collision. They are intersecting and combining their power.
McKAY: And – it’s headed right towards us.
WEIR: You just said the Ancients experienced these storms every twenty to thirty years. Atlantis must have some sort of precautions put in place.
McKAY: In the past, the Ancients have been protected by the shield or submerged deep enough in the water not to be affected.
SHEPPARD: OK – strike those options. What else have we got?
(Zelenka opens his hands uselessly. Rodney looks blank.)
ZELENKA: Nothing. It is a real threat. The high winds alone will wreak havoc.
SHEPPARD: C’mon guys! This city’s been around for a long time.
ZELENKA: Storm surge is inevitable.
McKAY: Not to mention the fact that by moving over a landmass just before hitting us, the likelihood of tornadoes and electrical activity is greatly increased.
SHEPPARD: This is Atlantis! I mean, they’ve gotta be able to handle that ... right?
McKAY (helplessly): No.
WEIR: Why not?
McKAY: The people who built this city knew they had a forcefield capable of holding back anything Mother Nature or, for that matter, the Wraith could throw at them. Without that protection, Atlantis is remarkably fragile.
ZELENKA: Even our conservative calculations project widespread structural damage.
McKAY: Flooding could sink the city entirely.
FORD: How could something as big as Atlantis just sink?
SHEPPARD: I’m sure the passengers on the Titanic were asking themselves the same question.
McKAY: Yes, well let’s not!
SHEPPARD: So what you’re saying is, if Teyla and I hadn’t discovered this, we ...
WEIR: We would be in even bigger trouble. (To Rodney and Zelenka) Alright, what’s the plan?
McKAY: By my calculations we have just under, what, twelve hours until the storm hits, so, uh, we plan to have a plan ...
ZELENKA: Yeah.
McKAY: ... by then.

LATER. John and Elizabeth are walking towards her office.
WEIR: We start investigating evacuation plans, both on the mainland and offworld somewhere.
SHEPPARD: You know McKay’ll come up with something. He’s just setting himself up to be a hero.
WEIR: Yeah, we know how Rodney is, but Doctor Zelenka – he seemed genuinely concerned.
SHEPPARD: So my orders are to come up with a friendly planet that wouldn’t mind putting us up for the night.
WEIR: Exactly. Take Ford, see what you can work out.

ATLANTIS MAINLAND. ATHOSIAN SETTLEMENT. The Athosians are preparing to abandon the settlement. Carson Beckett trudges towards Teyla, a heavy sack over one shoulder and a rope over the other.
BECKETT: I don’t know I have the right boots for this. I just meant to come out here and inoculate some wee babies.
TEYLA: We need all the hands we can spare before it comes. (Carson dumps the sack on the ground.) The storm could not only destroy our crops, our settlement could be washed away. If just a few of us were to remain ...
BECKETT: Crops can be replaced and homes rebuilt. People can’t.
TEYLA: Which is why we must do what we can ... now. (She tosses another rope to Carson who turns around, sighs, and trudges off again.)

MANARA (the planet which Weir mentioned Sergeant Bates had made a trading agreement with at the end of “Underground”). John and Aidan are seated at a table in a Council Chamber talking with the Manarian leader, Smeadon.
SMEADON: The entire population of Atlantis.
SHEPPARD: At most, yes.
FORD: Only for a day – two at most.
SMEADON: We are happy to trade with you for a share of our crops, but this ...
SHEPPARD: I know, it’s a lot to ask but ... I’m asking.
SMEADON: What do you offer in return?
SHEPPARD: I guess we’d owe you one.
SMEADON: One what?
SHEPPARD: A favour. (Smeadon looks round at his staff, confused.) Look, we’re in trouble. If you were a friend, you’ll help. If not, tell me now so I can ask somebody else.
SMEADON (thoughtfully): But who else would take in so many? (He looks at John.) I want something of value in return.
SHEPPARD: Oh, you do, do you?! Y’know, we can go find any uninhabited planet.
SMEADON: They’re usually uninhabited for a good reason, Major, and you know that as well as I do or you would not be here. Still, I’m sure you could find another world to take you in. You’re just so short on time.
SHEPPARD: One day you’re gonna run across a problem and you’re gonna need our help. (He looks at Aidan.) Isn’t that right, Lieutenant?
FORD: Yes sir. We’ve got lots of ships and weapons we can ... help with. (He nonchalantly but pointedly lays his rifle on the table.)
SMEADON: You’re telling me we can either be your friends or ...
SHEPPARD: I much prefer ‘friends’. That is of value to me. (He and Aidan stand up.) One night – two tops. We’ll bring our own blankets.
SMEADON: Very well. You may send your people.
SHEPPARD: This won’t be forgotten. We’ll go back – tell everybody the good news. We’ll send word once we know more.
SMEADON: I’ll look forward to it. (He doesn’t look like he’s looking forward to it at all.)
(John looks around suspiciously, then he and Aidan leave the room.)

ATLANTIS. LAB.
McKAY: No, no, no, no, no, I’ve already thought of that.
ZELENKA (gesturing to the scientist who just suggested something to Rodney): He may be onto something.
McKAY: I’ve already thought of it – it doesn’t ... Yes, the naqahdah generators could be used to power select sections of the city but when you subtract the areas that need to be secured just to protect themselves, it doesn’t leave much power to shield anything else and the city breaks apart because of a tidal swell.
ZELENKA: We could relocate some of them – put them closer together.
McKAY (sarcastically): You’re right – if only we had a magical tool that could slow down time. I foolishly left mine on Earth – did you bring yours?!
ZELENKA: You know, you’re not pleasant when you’re like this, McKay.
McKAY: I’m always like this.
ZELENKA: My point exactly.
(John and Aidan walk in.)
SHEPPARD: Well, I got a green light from Smeadon and the Manarians. I’m not sure how pleased he’ll be if we get stuck there, though. (He notices Rodney’s expression, which is not very confident.) That’s not gonna happen, though, right?
McKAY: Of course it’s not. We can always gate off to another planet.
SHEPPARD: Comforting! Thank you!
FORD: Are we sure there’s no part of the mainland we could go to?
(Elizabeth and Teyla come in.)
TEYLA: Everywhere that we’ve explored is in the path of the storm. My people are evacuating even now.
SHEPPARD: Still, Ford’s right. I mean, the mainland’s the size of North America. (To Rodney) You’re telling me the entire continent’s gonna get hit? It’s just I’d rather not owe Smeadon any favours.
WEIR: If we lose Atlantis we’ll be stuck on the mainland without any access to the Stargate.
SHEPPARD: Well, McKay will come up with something.
McKAY: I will try, but despite what you all may think, I am not Superman.
(John gives Rodney a long look, then looks around the room.)
SHEPPARD: Was anyone seriously thinking that?
(Elizabeth shakes her head. John looks at the other scientists in the room – one of them shakes his head minutely. John looks round at Aidan.)
FORD: No, sir.
ZELENKA: Never!
McKAY: Fine! My point is, the storm will affect over seventy percent of the mainland, and Atlantis isn’t safe either. If you want everyone to live, you gate them offworld.
(Everyone looks at each other, concerned.)

MANARIAN COUNCIL CHAMBER. Smeadon takes a device out of a drawer and switches it on. He sits down, activates a switch on the device and speaks into it.
SMEADON: Relay Station Two, prepare to receive transmission.
VOICE (from the device): RS Two awaiting transmission. Over.
SMEADON: I need you to relay a message to Cowen of the Genii. Tell him we have something to trade. (He smiles unpleasantly.)

ATLANTIS MAINLAND. The evacuation of the Athosians is continuing. Teyla is guiding people towards Puddlejumpers. The wind is getting strong.
FORD: This could be going faster.
TEYLA: Our people are hunters, Lieutenant – many returning from great distances. Others do not want to leave the settlement.
FORD: They know how serious this is.
TEYLA (raising her head into the wind): Even I would have a hard time believing in the strength of this coming storm if I did not see it from space.
FORD: Yeah, well, do what you can to speed things up.

ATLANTIS. LAB.
ZELENKA: In the Czech Republic we don’t have to deal with hurricanes.
McKAY: We don’t get that many in Canada either – except one called “Hazel”.
ZELENKA: “Hazel”?
McKAY: Mmm. Forty years ago.
ZELENKA: That’s interesting.
McKAY: Not really.
ZELENKA: No, not really.
McKAY: I was once almost struck by lightning.
ZELENKA: Lightning? (Inspired by a thought, he turns around to face Rodney just as Rodney jumps to his feet, obviously struck by the same thought.)

ATLANTIS CONTROL ROOM. Rodney and Zelenka hurry in and go over to Elizabeth.
McKAY: What is the one thing keeping us from having a shield?
WEIR: That would be ...
McKAY: Power. And what does the mega-storm from hell have lots of?
WEIR: Power.
McKAY: In the form of ...?
WEIR: You wanna build a windmill(!)
McKAY: Electricity.
ZELENKA: Atlantis is designed to withstand substantial lightning strikes. There are lightning rods all over the city.
McKAY: All those rods are channelled into four main grounding stations.
ZELENKA: In turn, those grounding stations discharge electricity back into the ocean, keeping Atlantis safe from massive electric shocks due to lightning strikes.
McKAY: Now, many of the hallways are lined with a superconductive material that allows a safe, low-voltage transfer of power throughout the city ...
ZELENKA: ... which of course means ...
McKAY: Yes, I’m getting there, I’m getting there. Let’s say the grounding stations weren’t around. Every time lightning struck the city, those halls would become supercharged.
WEIR: So, wait, you want ...
McKAY: If we were to disable the grounding stations ...
ZELENKA: ... which we think we can ...
McKAY: ... every time lightning struck the city, Atlantis would experience a momentary massive power surge.
ZELENKA: Now, that energy, if it’s channelled correctly ...
McKAY: ... yes, of course if channelled correctly – could conceivably be used to charge up the shield generator. Now, the more severe the storm, the more energy’s produced, and will keep the shield running.
ZELENKA: It’s an ingenious plan, really.
McKAY: I’m inclined to agree.
ZELENKA: The only downside is we have no way of storing all that energy.
McKAY: Ah, once the storm stops, the lightning stops striking ...
ZELENKA: Yeah, we have no way of charging up the generator.
McKAY: And we’re back to square one.
WEIR: So the city would survive.
McKAY: Mmm, it might give us a better than ninety percent ...
ZELENKA: ... seventy ...
McKAY: ... eighty percent chance.
WEIR: OK, so we should still evacuate.
McKAY: Yes, but not just because of Zelemka’s pessimism.
ZELENKA: Zelenka. If the plan works, the city will become highly charged with electricity. Really, the only safe place to be once the lightning begins to strike is ... in the Control Room.
McKAY: Mmm. We need to evacuate everyone offworld until the storm passes and execute the plan with the smallest team possible.
WEIR: OK, good. Get on it.
McKAY: Right. (He turns to Zelenka.) To the grounding stations.
ZELENKA: No, I think we should go to the power distribution centres first.
McKAY: Oh, good point, good call.
(They walk away, talking to each other.)

OFFWORLD SOMEWHERE. (We find out where in a moment.)
In what looks like a small fight arena, three people – two young men stripped to the waist, and one young woman – step forward, each of them holding a fighting staff. An older man dressed in black and wearing a black bandanna comes forward to face them. Simultaneously, the three younger people twirl their staffs in readiness for battle and cry out fiercely. We then recognise the woman – she is Sora of the Genii. They circle the older man, who stands impassively, waiting for their first move. They attack him simultaneously but despite the fact that he is unarmed, he wards off their blows with his arms and quickly wrestles a staff from one of the men. Despite their best efforts and even though they are attacking him together, in only a few seconds he has knocked both of the men to the floor. He and Sora circle each other cautiously. Eventually they attack each other but it’s fairly apparent that he’s only playing with her, making her work hard while he makes little effort. Finally he traps her hand between her own staff and his, pulling her towards him as she cries out in pain. Behind Sora, a man in Genii uniform comes into the arena and bows respectfully to the man, who uses the two staffs to flip Sora painfully to the ground.
MAN: Commander Kolya. Chief Cowen needs to see you immediately.
KOLYA: I’m not to be disturbed while training.
MAN (uncomfortably): He said immediately, sir.
(Kolya glares at him for a moment, then tosses one of the staffs to one of the fighters before reaching down to haul Sora to her feet. He gives her the other staff and leaves without a word.)

ATLANTIS MAINLAND. The wind is now much stronger than when we last saw the area. Teyla walks towards Aidan, who is waiting anxiously near the back of a Puddlejumper.
FORD: Still haven’t turned up yet?
TEYLA: I’m afraid not. They are on a hunting mission – no-one has been able to get them word about the evacuation.
(Carson comes over.)
FORD: How many again?
TEYLA: Three: two boys and a young woman.
BECKETT: Why don’t we just take our Jumper and go find ‘em?
TEYLA: They’re hunting in dense vegetation. Even if we were able to locate them, we would be unable to land.
BECKETT: Jumper Three is loaded and ready to go. Maybe you should just ...
TEYLA (interrupting): Just go. I will stay behind and give the hunters more time.
FORD (to Teyla): I’ll stay with you.
BECKETT: OK, I get the point. We’ll wait.

GENII OFFICE. Kolya, now in uniform, is standing facing Cowen, who is seated at a desk.
KOLYA: They’re not ready.
COWEN: Of course they are.
KOLYA: You commissioned me to train a group of men who on the most treacherous day guarded this facility or performed some sort of reconnaissance mission. They are not yet a strike force.
COWEN: This is the rarest of opportunities. Within the next hour there will be less than ten people on Atlantis, most of them only scientists. Now surely you can accomplish our goals and get out before the storm hits.
KOLYA: If all goes well – but we don’t train assuming all will go well.
COWEN: We cannot afford to pass up this opportunity.
KOLYA: You wanted my opinion – I gave it to you.
COWEN: And I value that opinion – but the Atlanteans are in possession of materials that are vital to our goal of defeating the Wraith. We need them. I need them. Ready your strike force.
(Kolya leaves the room.)

ATLANTIS. GATEROOM. The last of the crew are going through the Gate to Manara. As the last of them goes through, the Gate shuts down.
McKAY (in the Control Room): That’s everybody. We’ve got, uh, just over four and a half hours until the storm hits. Let’s get down to the labs.
(He and Elizabeth leave. John gives final instructions to two guards.)
SHEPPARD: Evacuate the people on inbound Jumper Two as soon as they come in.
GUARD: Yes, sir.
(Sheppard heads off after Elizabeth and Rodney.)

MANARIAN COUNCIL CHAMBER. Smeadon pours a drink into a goblet for a young Athosian sitting at the table. The young man is clearly drunk.
DORAN (slurred, pointing at the goblet): I’m finally at the point where I don’t mind the taste of it. (He giggles and lifts the goblet.)
SMEADON: I was raised on this brew – burned away whatever taste sense I had. So – you think you can teach our farmers a thing or two?
DORAN: Yes, yes, that’s what I was saying, yes. Most people think that farming is planting good seed in well-tilled soil, which it is. (Unseen by Doran, Sora and Kolya, in full uniform, come into the room. The Maniarians who were in the room leave.) It is! But there’s also more. And that knowledge is ... here. (He gestures to his own head.)
(Sora quietly walks up behind Doran.)
SMEADON: And you want to trade these marvellous skills in an exchange for a piece of my land?
DORAN (pointing drunkenly at Smeadon): I do.
SMEADON: I think I’ll need something more.
(Sora reaches round and grabs Doran’s pointing finger, crunching the bones as she wraps her other arm around his neck. He cries out in pain. Smeadon reaches forward and starts searching Doran’s clothing, eventually pulling out a GDO. He hands it to Kolya who has walked over to stand beside him.)
DORAN (looking at Kolya): Who are you?
KOLYA: Tell me the sequence of numbers to enter on this device.
DORAN (still held in a headlock by Sora): I can’t tell you that.
(Sora tightens her grip around his throat. He groans.)
SORA: It’s not worth dying for.
DORAN: You don’t-don’t understand. It’s my hand that you need to put in the code. That’s how it works.
KOLYA: And the shield of the Atlantis Stargate will be lowered?
DORAN: Yes, yes. (To Smeadon) What is this? Who are they?
KOLYA: Bring him to the Gate.
SMEADON: They’re friends, Doran.
KOLYA: Make sure he will enter the code.
SORA: He will.
SMEADON: Do what they say – and we’ll see about that piece of land.
(Sora hauls Doran to his feet and hustles him out of the room. Kolya comes round to face Smeadon, who rises to his feet.)
KOLYA: You’ve done a great service for the Genii, and will be rewarded. (Smeadon bows to him, and Kolya then leaves the room. Smeadon looks pleased with himself.)

ATLANTIS. LAB.
McKAY: There are dozens, possibly hundreds of lightning rods placed strategically around the city.
SHEPPARD: Wait a second.
McKAY: What?
SHEPPARD: Why?
McKAY: Why what?
SHEPPARD: Why are there hundreds of lightning rods placed around the city? Wouldn’t the shield protect against lightning?
McKAY: Yes, yes, it would, but running the shield all the time is only good for one thing – draining power.
SHEPPARD: Right.
McKAY: You’re aware that there’s a time element to what we’re doing here, right?
SHEPPARD: Yes, it’s been brought to my attention.
McKAY: Like I was saying, there are lightning rods – a lot of them – placed all over the city. Now, as it stands right now, all the energy they capture is routed into four main grounding stations. In turn the stations ground all that energy into the ocean below.
SHEPPARD: So instead of sending all that energy to ground ...
McKAY: ... we use it to power the shield.
WEIR: How?
McKAY: By directing it right down the corridors of Atlantis and into the shield generators.
WEIR: The city can handle that?
McKAY: Yes – theoretically.
SHEPPARD: Like dinosaurs turned into birds theoretically, or theory of relativity theoretically?
McKAY: What?! Uh, sort of between. Elizabeth – you take grounding station two; I’ll take grounding station one; Major – you take stations three and four.
SHEPPARD: Woah, woah, wait a second – where are stations three and four?
McKAY (indicating two points on a map of Atlantis): Here, and here. (The two points are at the edge of the city.)
SHEPPARD: And we are ...?
McKAY (indicating a point in the centre of the map): Here, yes. I need to get done quickly so I can start working on the subroutines, and Elizabeth was complaining about her knee the other day ...
SHEPPARD: Wait, wait, wait a second. Are these things even close to a transporter?
McKAY: Uh, yes, Elizabeth’s is.
SHEPPARD: And mine?
McKAY: Uh, it’s a brisk walk away.
SHEPPARD: And by ‘brisk’, you mean ... ‘far’.
McKAY: By ‘walk’, I mean ‘run’.
SHEPPARD: OK.
McKAY: You need to radio in once you’ve got to your first station.
SHEPPARD: Alright. Let’s do it.

ATLANTIS MAINLAND. The sky is now dark and the wind is fierce. It’s also raining heavily. The Athosian hunters have finally arrived and are running towards the Puddlejumper.
TEYLA: Hurry! Move! Come this way! Hurry!
(The hunters run inside the Jumper where Aidan is waiting.)
FORD: Everybody OK? Everybody OK? (He shows them where to sit.) OK, just stay here, strap in as best you can. It’ll be a real bumpy ride. (He runs forward, where Carson is sitting in the pilot’s seat, and takes the seat next to him.) Alright, let’s get out of here.
BECKETT: I’m not so certain it’s such a good idea any more.
FORD: What?!
BECKETT: Look at it out there. Even Major Sheppard would have a hard time flying through this.
(Teyla comes forward.)
TEYLA: We are ready.
BECKETT: I think it’s best if we wait it out. We’re safe as long as we’re in here. We’ve got rations, and we have plenty of water.
FORD: Yeah, especially outside!
(Carson looks round to Teyla, who looks at the storm raging outside the front windscreen.)
TEYLA: Very well. I hope you’re right, Doctor. We will not have a chance to change our minds if you are wrong.
(Carson turns and looks at the rain lashing down on the windscreen.)
BECKETT: It’ll be cosy.

ATLANTIS. GROUNDING STATION FOUR. John arrives and opens the door to the grounding station. He pauses at the sound of a strong wind blowing. The area is exposed to the outside and he is buffeted as he walks forward. He walks to the balcony, then activates his radio.
SHEPPARD (shouting to be heard over the wind): I’m here!
McKAY (over radio): I told you to contact me when you got to the first one, Major.
SHEPPARD: I am at the first one, Rodney!
McKAY: Oh, sorry. I’ve already done mine.
SHEPPARD: That’s great! Good for you!
WEIR (over radio): Me too.
SHEPPARD: Good for everyone!
McKAY: Where are you now?
SHEPPARD: I’m at the damned grounding station!
McKAY: No, no, no, no, not you.
WEIR: I’m in the transporter.
(Near to where Rodney is walking, a transporter door opens and Elizabeth walks out and joins him.)
McKAY: There you are.
WEIR: There I am.
SHEPPARD: Glad everybody’s having such a good time. What do I do?
McKAY: There should be a keypad right on the console of the station.
(John walks away from the balcony and goes over to the station.)
SHEPPARD: Got it.
McKAY: Punch in the Ancient equivalent of oh three one five four seven. (John starts to do so.) That do it?
(John finishes punching in the code, and the grounding rod at the edge of the station separates into two pieces. Beyond it, we can see a huge black cloud approaching the base.)
SHEPPARD: Yeah!
McKAY: Good. Three down, one to go. They all seem to have the same separation code, so get to the next one, repeat the procedure. We’ll meet you in the Control Room.
SHEPPARD: Roger that. (He runs off.)

CONTROL ROOM. The two guards are leaning on the balcony overlooking the Gate.
GUARD 1: Bacon.
GUARD 2: The one thing you wish you brought with you is bacon?
GUARD 1: Hey, it’s the food that makes other food worth eating.
GUARD 2: You wish you brought bacon to another galaxy?
GUARD 1: Yeah, you asked me ... (Behind them, the Gate starts to dial in.) Offworld activation.
(The two of them run to the control panel.)
GUARD 2: Doctor Weir said no-one should be coming back ...
WOMAN’s VOICE (over comms): There’s been an attack on Manara. We’ve got wounded incoming. Lower the shield.
GUARD 1 (looking at the console): They’re broadcasting an Athosian IDC.
WOMAN’s VOICE: Please, before it’s too late!
GUARD 1 (into comms): We are lowering the shield.
GUARD 2: Oh, skip the OK from Doctor Weir!
GUARD 1: They’re under attack. Lower the shield.
(Guard 2 looks at him for a moment, then punches in the code to lower the shield. The two of them run for the stairs as Guard 2 speaks into his radio.)
GUARD 2 (into radio): Doctor Weir, there’s been some sort of an attack from Manara. We have an Athosian party incoming with wounded.
WEIR: We’re on our way. (She and Rodney start running towards the Gateroom.)

GATEROOM. Several people dressed in cloaks come through the Gate. One of them is Sora. Two men are carrying someone on a stretcher who is covered with a blanket. The guards run down the steps to meet them.
GUARD 1: What happened?
SORA: They were everywhere. I can’t believe they didn’t kill us all.
GUARD 1: Who?
(Kolya, who was under the blanket on the stretcher, rolls off the stretcher and shoots the two guards with a pistol. The other people take off their cloaks – they are wearing Genii uniforms underneath. Sora watches as a man checks the two guards. She looks at Kolya, not happy that he has killed them.)
KOLYA: Secure the room.
SORA: These men could have been overpowered. We need the Atlanteans to be co-operative.
KOLYA (gazing around the Gateroom): Secure the room. (He walks away. Sora looks at him for a moment, then turns to the rest of her people.)
SORA: Cover the entrances!
(People run to comply. Kolya walks partway up the steps and then turns to look around the Gateroom with a look of satisfaction on his face. Sora looks at him, concerned at his expression.)

Elsewhere on the base, John is running towards Grounding Station Three. Elizabeth reports over the radio.
WEIR (over radio): Apparently there’s wounded incoming.
SHEPPARD (stopping running for a moment): Doesn’t make any sense. They said it was Wraith-related?
WEIR: We’ll ask them ourselves in a second – hold on. (She and Rodney arrive at the Gateroom to find the Genii soldiers waiting for them.) What the hell is going on?
(The soldiers grab them, pointing guns at them.)
(John starts running again.)
(In the Gateroom, Kolya comes down the steps towards Elizabeth and Rodney.)
KOLYA: Doctor Elizabeth Weir.
WEIR: Yes.
KOLYA (looking at Rodney): And you must be Doctor McKay.
(Rodney doesn’t answer, but Sora comes over to Kolya’s side.)
SORA: That is him.
KOLYA: Where is Major Sheppard? (We see John running – he is still receiving radio transmissions so can hear what’s happening in the Gateroom.) I would like to know the whereabouts of Major Sheppard.
WEIR: You seem to know a lot about us. Who are you?
McKAY: They’re Genii.
KOLYA: There’s only one thing you need to know, Doctor Weir. As of right now, we are in control of Atlantis.

LATER. JUMPER BAY. John opens the rear door of a Puddlejumper and checks out the interior before walking inside. As the lights automatically come on, John obviously thinks of what he needs because a panel opens near the pilot’s seat and a lifesigns detector is inside. He takes it and then activates the comms.
SHEPPARD (into comms): Jumper Two, this is Sheppard, come in. ... Jumper Two, do you copy?
(We see Jumper Two still on the ground on the mainland, being lashed by the storm. Lightning flashes frequently and loud thunder can be heard.)
FORD (into comms): This is Ford, sir. We decided to wait out the storm in the Jumper.
SHEPPARD: You’re still on the mainland?
FORD: Yes, sir.
SHEPPARD: We’ve got a situation here. From what I can ascertain, a small Genii strike force has gated in.
FORD: The Genii?! The folks who wanted us to build them an A-bomb?
SHEPPARD: Yeah, that’s them, and they’ve got Weir and McKay hostage. They’ve also got control of the Gateroom.
FORD: You’re breaking up, sir – did you say hostage?
SHEPPARD: Affirmative.
BECKETT: Ah, no!
FORD: We’re on our way. (He turns to the control panel.)
BECKETT: What d’you think you’re doing?
FORD: You heard him!
BECKETT: Take a look outside, hot shot. We’re not flying through this.
FORD: McKay and Weir were taken hostage, Doc. I’m not just gonna sit here and do nothing.
BECKETT: Neither one of us are real pilots. It was a bad idea an hour ago – it’s an idiotic one now.
FORD: We’re gonna have to take our chances.
TEYLA: Doctor Beckett is right, Lieutenant – you are of no use to Major Sheppard dead. (Into comms) Major, this is Teyla. (Although John can hear most of her message, it’s slightly garbled by static.) The hurricane is in full force outside. We could attempt to fly through it but it is doubtful that we could make it back to Atlantis; and we have three young passengers.
SHEPPARD: That’s bad news.
TEYLA: I’m sorry.
SHEPPARD: So am I. Just stay put til it passes over.
FORD: Sir ...
SHEPPARD: It’s OK, Lieutenant. Just get your ass back here as soon as you can. I could use a little back-up.
FORD: Good luck, sir.

ATLANTIS GATEROOM. Kolya is outside on the balcony looking at the approaching storm. He goes back inside, where the body of one of the dead guards is being stretchered out of the room. He walks over to Elizabeth and Rodney, who are watching their dead colleague being taken away. Kolya walks around them, looking round the room.
WEIR: Who are you?
KOLYA: Commander Acastus Kolya of the Genii. This Atlantis is extraordinary – more than I ever imagined.
WEIR: What have you done with the rest of my people?
KOLYA: I’m quite sure they have no idea we’re even here.
WEIR: Then they’re safe?
KOLYA: Yes.
WEIR: How were you able to bypass the shield?
KOLYA: With a time-tested combination of strong drink and a weak mind.
WEIR (stepping forward): There was a time when our two peoples considered becoming allies. Why are you doing this?
KOLYA: You’re in possession of supplies we vitally need. Hand them over without difficulty and we’ll leave peacefully.
WEIR: Or?
KOLYA: We’re both intelligent people, Doctor Weir. I’m sure there’s no need for me to demonstrate once again the strength of my resolve.
WEIR: Which supplies did you have in mind?
KOLYA: All of your stores of the C4 explosive, all of your medical supplies, the Wraith data device you stole from my people, and one of your ships.
McKAY: Is that all?(!)
KOLYA: No. Where is Major Sheppard?
WEIR: He’s on the mainland. What you’re asking for is not easy. We’ve had to divert a lot of power in order to prepare for the storm. The armoury’s safety doors have shut, which means we can’t ...
(Kolya holds up a hand to stop her.)
KOLYA: I know a lie.
(Rodney leans forward to address Elizabeth, and puts his hands on the console in front of him to brace himself.)
McKAY: Elizabeth, just give him what he needs. (We see John coming out of the Puddlejumper – he can now heard what Rodney is saying.) He needs the C4, the medical supplies and the Wraith data device – just give them to him. None of that’s worth dying for.
(In the Control Room, one of the Genii soldiers sees what Rodney is doing and steps forward for a better look. One of Rodney’s hands is holding down buttons on the console. Kolya sees what the soldier is looking at.)
KOLYA: Step away from the console.
(Rodney raises his hands off the console.)
McKAY: I was leaning. I was just leaning.
WEIR (to Kolya): Your request is unreasonable. And you can’t possibly need all our C4, all our medical supplies.
KOLYA: You’re in no position to tell me what is reasonable and what is not.
WEIR: How do we know that you won’t kill us once we give you what you need?
KOLYA: You don’t. Please show my men where they can find what they are looking for. (He nods to Sora and some of the other soldiers, who take Elizabeth by the arms and hustle her away. Kolya steps closer to Rodney.) What are you doing here?
McKAY: My understanding – I’m being held hostage.
KOLYA: I mean here in Atlantis. Why did some of you stay behind?
McKAY: Oh. I was helping with things.
KOLYA: Like what?
McKAY: You know – make sure everyone got out OK.
KOLYA: Isn’t that the work of someone ... less important?
McKAY (laughing nervously): You’d think so, wouldn’t you?
KOLYA: You have a plan, don’t you?
McKAY: I’ve got lots of plans about lots of things.
KOLYA: I’m interested in the plan you have to save the city.
McKAY: I never said anything about saving anything.
(Kolya puts his hand on Rodney’s shoulder.)
KOLYA: Not yet. (He nods to a soldier standing behind Rodney, who draws out a long sharp knife. Rodney looks at it in dread.)

STORAGE ROOM. Genii guards are taking cartons and packages off the shelves.

LAB. Sora and other soldiers are walking around looking at displays. Elizabeth takes out a small case and puts it on the table. Sora walks over to her.
SORA: Where is Teyla Emmagan?
WEIR: You know Teyla?
SORA: Is she here? In the city?
WEIR: No, she isn’t. (Sora looks away, disappointed.) You must be Sora. I read the Genii mission report – I’m sorry about your father.
SORA: He’ll be avenged.
WEIR: Teyla didn’t kill him.
SORA: No – she left him to die.
WEIR: She had no choice ...
SORA (angrily): Are you finished?
(Elizabeth looks at her, then opens the case and takes out the Wraith data device.)
WEIR: All of the information we downloaded from the Wraith ship is still on this device. (She hands it to Sora.)

ARMOURY. Genii soldiers walk into the armoury and look around at the weapons stored there. The camera pans over to boxes labelled “C4 Explosives”. The boxes are empty. One of the soldiers goes over to the boxes and sees a radio standing in the middle of one of the empty boxes. He picks it up, looks at it, then looks over his shoulder to his colleague.

CONTROL ROOM. The soldier hands the radio to Kolya. Nearby, Elizabeth is examining Rodney’s right arm. The sleeve is slashed and his arm is covered in blood. Rodney is whimpering quietly.
WEIR: What did they do to you?
McKAY: I tried to keep my mouth shut, I tried – I just couldn’t ... (He trails off as Kolya approaches and holds up the radio.)
KOLYA: What’s the meaning of this?
WEIR: I honestly have no idea.
McKAY: It’s a radio. The arrow points to the ‘talk’ button.
(Kolya activates the button and holds the radio to his mouth.)
KOLYA: This is Commander Kolya.
SHEPPARD (elsewhere in the base): Kolya – that’s a hard name to pronounce. Is that a first name? My name’s Major John Sheppard and I have hidden the C4 where you will never – I repeat, never – find it. When I get confirmation that the prisoners have been safely released and allowed to gate off Atlantis, I will help you find it.
KOLYA (to Elizabeth and Rodney): He’s good.
WEIR: Yes, he is. I’d do what he says.
KOLYA (into radio): Your offer is very generous, Major.
SHEPPARD: Yes, it is.
KOLYA: However, Doctor McKay recently shared with me there’s a plan in action to save the city.
SHEPPARD: He did?!
KOLYA: He did. My understanding is there is one final grounding station that needs to be deactivated. Uncouple the grounding rods at Station Three, assist with the reactivation of the shield, and you and your friends can leave here unharmed.
SHEPPARD: Wait a minute – I thought all you wanted was C4 and a Jumper.
KOLYA: Why raid a city when you can seize it, Major? Atlantis will be ours or the ocean’s. You choose.

ATLANTIS MAINLAND. The storm is still lashing the Jumper.
FORD: We should have heard something from the Major by now.
TEYLA: Perhaps he has not had the opportunity.
FORD: I don’t like not knowing what’s going on in there.
BECKETT: Why would the Genii attack us? Why now?
FORD: We didn’t exactly leave on the best terms. I mean, aside from the fact that we stole some of their gear, and didn’t hand over the C4 we promised them, they’re pretty convinced Teyla killed one of their top guys.
TEYLA: They believe so falsely. The fact that they chose our weakest hour cannot be a coincidence. Someone must have told them that we would be in a diminished capacity.
FORD: There’s gotta be a way back. (He looks at the control console.)
BECKETT: Those winds outside are blowing at a hundred and ten knots. We’re not going anywhere, son.

ATLANTIS. ELIZABETH’S OFFICE. Kolya is sitting behind the desk looking at information padds. Sora escorts Elizabeth in.
WEIR: Thank you for seeing me. This city was designed to be inhabited by the Ancients and their direct descendants and although, yes, while there is limited functionality for those who do not possess the Ancient gene, it is only those who have it who can revive the city to its true potential.
KOLYA: And you have this gene?
WEIR: No, but many of my team do. The Wraith are slowly waking. Soon this entire galaxy will be embroiled in a war the likes of which our generations have never seen.
KOLYA: A war that you expedited.
WEIR: Disagreements like ours will no longer matter. The only thing of any consequence will be how prepared we are and what defence we are able to mount. Now, this city holds many secrets which will help us win that war – but only if my team are here to discover them. So, fine, take whatever you need for your people, but if you don’t leave us this city you’re only hurting yourselves in the long run.
KOLYA: You believe your people – who are not even of this galaxy – are closer to the Ancients than we are? Your arrogance is astounding. We will take this city, we will mount a defence, and we will win – with or without your help, Doctor Weir.
(A Genii private arrives.)
PRIVATE: Sir, he’s at the grounding station.
(Kolya stands and leave the room.)

GROUNDING STATION THREE. John opens the doors and walks in. He checks his lifesigns detector and looks concerned at what he sees on the screen.

CONTROL ROOM. A Genii man speaks into a comms unit.
MAN (into comms): The commander’s here.
(Kolya walks over to the man)
SOLDIER (over comms): He’s just standing there, sir.
KOLYA: (into comms): Hold your position. Do not approach until he’s finished.
SOLDIER: Yes, sir.
KOLYA: Use lethal force only if necessary.
SORA (to Kolya): You told him he would be unharmed.
KOLYA: Let’s hope he doesn’t put up much of a fight.

GROUNDING STATION THREE. We now see what John can see on the lifesigns detector – he can see his own signal, and two other signals just outside the door. He moves around the control console and stands on the other side facing the door, then moves to the side wall where there is better cover.

GROUNDING STATION THREE. John, his rifle raised, walks carefully towards the door. Outside, the two Genii soldiers are cautiously lurking around trying to see where he is. One nods to the other, who nods back. One of them runs inside the room and starts firing. John shoots him, then takes cover against the wall by the door. He checks his lifesigns detector again. The other soldier is just the other side of the wall. John runs deeper into the room as the second soldier runs in. The soldier fires at John, who is running towards the balcony. The soldier’s shots hit the control console as John dives over the balcony and onto a ledge just below, then rises up and shoots the soldier. John comes back over the balcony and runs to check that the soldiers are down, then takes a communications device from one of them before going over to the control console. The panel is shot to bits and is sparking. He speaks into the communications device.
SHEPPARD (into comms): Let me tell you what you did wrong here, Kolya. A: you lost two of your men. B: you damaged the switch before I could separate the grounding rods, which I’m sure you’re gonna get an earful from McKay for; and C: you lost all of what little credibility you had with me.
(In the Control Room.)
McKAY: D’you have any idea of how big a setback that is? I may not even be able to activate the shield. I mean, I can’t possibly ... (the soldier grabs his injured arm again) get off me!
KOLYA (into comms): You killed two of my men.
SHEPPARD: I guess we’re even!
KOLYA: I don’t like even. (He pulls a pistol out of his coat.)
SHEPPARD: I’m not finished yet!
KOLYA: Neither am I. Say goodbye to Doctor Weir. (He points his pistol at Elizabeth.)
SHEPPARD: The city has a self-destruct button. You hurt her, I’ll activate it. Nobody’ll get Atlantis.
KOLYA: Even if it exists, Major, you need at least two senior personnel to activate it – and I’m about to take one of them out of the equation. (He looks at Elizabeth who stares, terrified, at him and the pistol he is pointing at her.)
(In Grounding Station Three)
SHEPPARD: Kolya?! (Kolya doesn’t reply.) Kolya?! (Again, no reply.) I’ll give you a ship! I’ll fly it out of here for you myself! (There’s silence from the comms as we see the huge storm cloud approaching the base. John screams into the comms device.) KOLYA!!
(Outside the base, the front edge of the rainstorm is just minutes away from the base as the words we just love to see appear on the screen.)